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Iron in PDB 7w3e: Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

Enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K

All present enzymatic activity of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K:
1.9.3.1; 7.1.1.9;

Protein crystallography data

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e was solved by T.Tsukihara, A.Shimada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.76 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.666, 203.752, 177.683, 90, 90, 90
R / Rfree (%) 16.2 / 18.2

Other elements in 7w3e:

The structure of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K also contains other interesting chemical elements:

Sodium (Na) 4 atoms
Magnesium (Mg) 2 atoms
Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K (pdb code 7w3e). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K, PDB code: 7w3e:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 7w3e

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Iron binding site 1 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:21.8
occ:1.00
 FE A:HEA601 0.0 21.8 1.0
NE2 A:HIS61 2.0 20.3 1.0
NE2 A:HIS378 2.0 21.3 1.0
ND A:HEA601 2.0 21.1 1.0
NC A:HEA601 2.0 21.1 1.0
NA A:HEA601 2.0 22.0 1.0
NB A:HEA601 2.0 22.2 1.0
CE1 A:HIS378 2.9 23.4 1.0
CE1 A:HIS61 2.9 23.0 1.0
C4D A:HEA601 3.0 20.1 1.0
CD2 A:HIS61 3.0 22.6 1.0
C4B A:HEA601 3.0 21.0 1.0
C4A A:HEA601 3.0 21.9 1.0
C1D A:HEA601 3.0 20.6 1.0
C4C A:HEA601 3.0 21.3 1.0
C1B A:HEA601 3.1 22.4 1.0
C1C A:HEA601 3.1 20.6 1.0
C1A A:HEA601 3.1 21.0 1.0
CD2 A:HIS378 3.1 24.4 1.0
CHD A:HEA601 3.4 23.1 1.0
CHC A:HEA601 3.4 21.4 1.0
CHA A:HEA601 3.4 22.1 1.0
CHB A:HEA601 3.4 23.9 1.0
ND1 A:HIS378 4.1 22.3 1.0
ND1 A:HIS61 4.1 21.5 1.0
CG A:HIS61 4.1 21.4 1.0
CG A:HIS378 4.2 20.6 1.0
C2C A:HEA601 4.2 21.2 1.0
C3D A:HEA601 4.2 19.9 1.0
C3A A:HEA601 4.2 21.2 1.0
C2A A:HEA601 4.2 21.8 1.0
C2D A:HEA601 4.2 21.5 1.0
C3B A:HEA601 4.3 20.9 1.0
C2B A:HEA601 4.3 21.9 1.0
C3C A:HEA601 4.3 20.2 1.0
OG A:SER382 4.6 26.5 0.2
OG A:SER382 5.0 23.4 0.6

Iron binding site 2 out of 6 in 7w3e

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Iron binding site 2 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:21.2
occ:0.52
 FE A:HEA602 0.0 21.2 0.5
ND A:HEA602 1.0 26.4 0.5
FE A:HEA602 1.1 20.4 0.5
NC A:HEA602 1.9 21.1 0.5
C A:CYN606 1.9 25.2 0.5
C1D A:HEA602 2.0 21.8 0.5
ND A:HEA602 2.0 19.2 0.5
NA A:HEA602 2.0 21.1 0.5
NB A:HEA602 2.0 23.1 0.5
NC A:HEA602 2.1 20.2 0.5
NE2 A:HIS376 2.2 25.6 1.0
C A:CYN606 2.2 17.8 0.5
C4D A:HEA602 2.3 19.3 0.5
C4C A:HEA602 2.5 22.5 0.5
CHD A:HEA602 2.6 18.4 0.5
NA A:HEA602 2.6 20.4 0.5
N A:CYN606 3.0 24.9 0.5
C4D A:HEA602 3.0 20.6 0.5
C1A A:HEA602 3.0 21.4 0.5
C1D A:HEA602 3.1 21.1 0.5
C1B A:HEA602 3.1 23.8 0.5
C4A A:HEA602 3.1 20.8 0.5
C4B A:HEA602 3.1 21.2 0.5
CD2 A:HIS376 3.1 23.3 1.0
NB A:HEA602 3.1 18.8 0.5
C1C A:HEA602 3.1 22.5 0.5
C4C A:HEA602 3.1 21.2 0.5
CHA A:HEA602 3.2 17.5 0.5
N A:CYN606 3.2 18.8 0.5
C2D A:HEA602 3.2 18.5 0.5
C1C A:HEA602 3.2 20.8 0.5
C1A A:HEA602 3.2 18.5 0.5
CE1 A:HIS376 3.3 26.1 1.0
C3D A:HEA602 3.4 21.9 0.5
CHA A:HEA602 3.5 25.1 0.5
CHC A:HEA602 3.5 19.6 0.5
CHB A:HEA602 3.5 25.5 0.5
CHD A:HEA602 3.5 21.0 0.5
C3C A:HEA602 3.8 21.2 0.5
C4A A:HEA602 3.8 23.4 0.5
C4B A:HEA602 4.0 19.6 0.5
CHC A:HEA602 4.0 19.7 0.5
C1B A:HEA602 4.2 19.0 0.5
C3D A:HEA602 4.2 21.3 0.5
C2C A:HEA602 4.2 17.6 0.5
C2A A:HEA602 4.2 21.8 0.5
C3B A:HEA602 4.2 19.6 0.5
C2D A:HEA602 4.3 22.0 0.5
CG A:HIS376 4.3 21.8 1.0
C2B A:HEA602 4.3 19.8 0.5
C3A A:HEA602 4.3 21.9 0.5
C2C A:HEA602 4.3 17.8 0.5
C3C A:HEA602 4.3 23.1 0.5
ND1 A:HIS376 4.3 23.7 1.0
CHB A:HEA602 4.5 19.1 0.5
CMD A:HEA602 4.5 22.7 0.5
CG1 A:VAL380 4.6 22.9 0.6
C2A A:HEA602 4.6 21.8 0.5
CG1 A:VAL380 4.6 22.7 0.2
CAD A:HEA602 4.8 21.0 0.5
C3A A:HEA602 4.8 20.8 0.5
CAC A:HEA602 5.0 20.2 0.5

Iron binding site 3 out of 6 in 7w3e

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Iron binding site 3 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:20.4
occ:0.48
 FE A:HEA602 0.0 20.4 0.5
FE A:HEA602 1.1 21.2 0.5
NB A:HEA602 1.1 23.1 0.5
NA A:HEA602 1.8 21.1 0.5
C1B A:HEA602 2.0 23.8 0.5
NB A:HEA602 2.0 18.8 0.5
NC A:HEA602 2.0 21.1 0.5
NA A:HEA602 2.0 20.4 0.5
ND A:HEA602 2.0 26.4 0.5
NE2 A:HIS376 2.0 25.6 1.0
C A:CYN606 2.1 17.8 0.5
C A:CYN606 2.4 25.2 0.5
C4A A:HEA602 2.4 20.8 0.5
C4B A:HEA602 2.5 21.2 0.5
CHB A:HEA602 2.5 25.5 0.5
NC A:HEA602 2.7 20.2 0.5
CE1 A:HIS376 2.9 26.1 1.0
C4A A:HEA602 3.0 23.4 0.5
C1C A:HEA602 3.0 20.8 0.5
C4B A:HEA602 3.0 19.6 0.5
C1B A:HEA602 3.0 19.0 0.5
C4C A:HEA602 3.1 22.5 0.5
C1A A:HEA602 3.1 18.5 0.5
C4D A:HEA602 3.1 19.3 0.5
ND A:HEA602 3.1 19.2 0.5
C1D A:HEA602 3.1 21.8 0.5
CD2 A:HIS376 3.2 23.3 1.0
C1A A:HEA602 3.2 21.4 0.5
N A:CYN606 3.2 18.8 0.5
C2B A:HEA602 3.2 19.8 0.5
N A:CYN606 3.3 24.9 0.5
CHC A:HEA602 3.3 19.6 0.5
C3B A:HEA602 3.4 19.6 0.5
C1C A:HEA602 3.4 22.5 0.5
CHC A:HEA602 3.4 19.7 0.5
CHB A:HEA602 3.5 19.1 0.5
CHA A:HEA602 3.5 17.5 0.5
CHD A:HEA602 3.6 18.4 0.5
C3A A:HEA602 3.8 21.9 0.5
C4D A:HEA602 3.9 20.6 0.5
C4C A:HEA602 4.0 21.2 0.5
CHA A:HEA602 4.0 25.1 0.5
ND1 A:HIS376 4.1 23.7 1.0
C2A A:HEA602 4.1 21.8 0.5
C1D A:HEA602 4.2 21.1 0.5
C3A A:HEA602 4.2 20.8 0.5
CG A:HIS376 4.2 21.8 1.0
C3C A:HEA602 4.2 21.2 0.5
C2A A:HEA602 4.2 21.8 0.5
C2B A:HEA602 4.2 23.0 0.5
C3B A:HEA602 4.3 21.4 0.5
C2C A:HEA602 4.3 17.6 0.5
C2D A:HEA602 4.3 18.5 0.5
C3D A:HEA602 4.3 21.9 0.5
O A:HOH822 4.5 22.9 0.7
CMB A:HEA602 4.5 25.3 0.5
CA A:GLY355 4.6 26.0 1.0
CHD A:HEA602 4.6 21.0 0.5
C2C A:HEA602 4.8 17.8 0.5
NE2 A:HIS290 4.8 18.3 0.5
CG1 A:VAL380 4.9 22.9 0.6
C11 A:HEA602 4.9 23.2 0.5
CMA A:HEA602 5.0 19.8 0.5

Iron binding site 4 out of 6 in 7w3e

Go back to Iron Binding Sites List in 7w3e
Iron binding site 4 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:25.1
occ:1.00
 FE N:HEA601 0.0 25.1 1.0
NE2 N:HIS378 2.0 25.5 1.0
NC N:HEA601 2.0 25.5 1.0
NE2 N:HIS61 2.0 23.9 1.0
NB N:HEA601 2.0 25.6 1.0
NA N:HEA601 2.0 25.7 1.0
ND N:HEA601 2.0 23.9 1.0
CE1 N:HIS378 2.9 28.9 1.0
CE1 N:HIS61 3.0 27.1 1.0
C4B N:HEA601 3.0 24.1 1.0
C4A N:HEA601 3.0 26.7 1.0
C1D N:HEA601 3.0 25.1 1.0
CD2 N:HIS61 3.0 24.4 1.0
CD2 N:HIS378 3.0 25.4 1.0
C4C N:HEA601 3.0 23.6 1.0
C1B N:HEA601 3.0 26.9 1.0
C4D N:HEA601 3.0 24.5 1.0
C1A N:HEA601 3.1 23.9 1.0
C1C N:HEA601 3.1 24.7 1.0
CHC N:HEA601 3.4 25.2 1.0
CHD N:HEA601 3.4 24.9 1.0
CHB N:HEA601 3.4 28.1 1.0
CHA N:HEA601 3.5 26.6 1.0
ND1 N:HIS378 4.0 28.6 1.0
ND1 N:HIS61 4.1 25.6 1.0
CG N:HIS378 4.1 25.1 1.0
CG N:HIS61 4.2 24.2 1.0
C3A N:HEA601 4.2 24.8 1.0
C2D N:HEA601 4.2 23.9 1.0
C2B N:HEA601 4.2 24.6 1.0
C3C N:HEA601 4.3 24.5 1.0
C3D N:HEA601 4.3 24.5 1.0
C3B N:HEA601 4.3 24.8 1.0
C2A N:HEA601 4.3 25.1 1.0
C2C N:HEA601 4.3 24.4 1.0
OG N:SER382 4.5 32.6 0.3
CE2 N:PHE377 5.0 28.1 1.0

Iron binding site 5 out of 6 in 7w3e

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Iron binding site 5 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:22.9
occ:0.62
 FE N:HEA602 0.0 22.9 0.6
ND N:HEA602 1.1 23.8 0.4
FE N:HEA602 1.2 21.3 0.4
C1D N:HEA602 1.8 20.1 0.4
NC N:HEA602 1.8 21.0 0.4
C N:CYN606 1.9 28.9 0.6
NA N:HEA602 2.0 23.9 0.6
NC N:HEA602 2.0 20.4 0.6
ND N:HEA602 2.0 21.7 0.6
NB N:HEA602 2.0 23.1 0.6
NE2 N:HIS376 2.1 27.0 1.0
C N:CYN606 2.3 20.2 0.4
C4C N:HEA602 2.4 27.4 0.4
C4D N:HEA602 2.4 20.7 0.4
CHD N:HEA602 2.5 22.6 0.4
NA N:HEA602 2.7 24.9 0.4
C1A N:HEA602 3.0 21.4 0.6
N N:CYN606 3.0 26.4 0.6
C1B N:HEA602 3.0 25.9 0.6
C4D N:HEA602 3.0 24.3 0.6
C1D N:HEA602 3.0 23.1 0.6
C4A N:HEA602 3.0 21.9 0.6
C1C N:HEA602 3.1 19.4 0.6
C4B N:HEA602 3.1 20.2 0.6
C4C N:HEA602 3.1 23.1 0.6
CD2 N:HIS376 3.1 25.6 1.0
C2D N:HEA602 3.1 21.5 0.4
C1C N:HEA602 3.1 20.2 0.4
NB N:HEA602 3.2 21.3 0.4
CE1 N:HIS376 3.2 29.9 1.0
N N:CYN606 3.3 24.9 0.4
CHA N:HEA602 3.4 22.7 0.4
C1A N:HEA602 3.4 19.6 0.4
C3D N:HEA602 3.4 22.7 0.4
CHA N:HEA602 3.5 25.2 0.6
CHC N:HEA602 3.5 21.8 0.6
CHD N:HEA602 3.5 22.4 0.6
CHB N:HEA602 3.5 25.3 0.6
C3C N:HEA602 3.7 23.6 0.4
C4A N:HEA602 3.9 20.4 0.4
C4B N:HEA602 4.0 23.3 0.4
CHC N:HEA602 4.0 21.6 0.4
C2C N:HEA602 4.1 19.0 0.4
C2A N:HEA602 4.2 22.6 0.6
C3A N:HEA602 4.2 21.1 0.6
C3D N:HEA602 4.2 22.9 0.6
C1B N:HEA602 4.2 20.8 0.4
C2D N:HEA602 4.2 22.6 0.6
C2B N:HEA602 4.2 22.9 0.6
C3B N:HEA602 4.3 21.2 0.6
CG N:HIS376 4.3 25.0 1.0
C2C N:HEA602 4.3 19.4 0.6
C3C N:HEA602 4.3 21.7 0.6
ND1 N:HIS376 4.3 28.2 1.0
CMD N:HEA602 4.3 23.4 0.4
CG1 N:VAL380 4.6 27.9 0.4
CHB N:HEA602 4.6 22.4 0.4
CG1 N:VAL380 4.6 27.9 0.3
C2A N:HEA602 4.7 21.1 0.4
CAD N:HEA602 4.8 28.6 0.4
CAC N:HEA602 4.9 19.7 0.4
C3A N:HEA602 5.0 22.9 0.4

Iron binding site 6 out of 6 in 7w3e

Go back to Iron Binding Sites List in 7w3e
Iron binding site 6 out of 6 in the Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:21.3
occ:0.38
 FE N:HEA602 0.0 21.3 0.4
NB N:HEA602 1.2 23.1 0.6
FE N:HEA602 1.2 22.9 0.6
NA N:HEA602 1.8 23.9 0.6
C1B N:HEA602 1.9 25.9 0.6
NB N:HEA602 2.0 21.3 0.4
NA N:HEA602 2.0 24.9 0.4
NC N:HEA602 2.0 21.0 0.4
ND N:HEA602 2.0 23.8 0.4
NE2 N:HIS376 2.1 27.0 1.0
C N:CYN606 2.1 20.2 0.4
C4A N:HEA602 2.3 21.9 0.6
C N:CYN606 2.4 28.9 0.6
CHB N:HEA602 2.4 25.3 0.6
C4B N:HEA602 2.5 20.2 0.6
NC N:HEA602 2.8 20.4 0.6
CE1 N:HIS376 2.9 29.9 1.0
C1C N:HEA602 3.0 20.2 0.4
C4A N:HEA602 3.0 20.4 0.4
C1B N:HEA602 3.0 20.8 0.4
C1D N:HEA602 3.0 20.1 0.4
C4B N:HEA602 3.0 23.3 0.4
C4C N:HEA602 3.1 27.4 0.4
C1A N:HEA602 3.1 19.6 0.4
C1A N:HEA602 3.1 21.4 0.6
C4D N:HEA602 3.1 20.7 0.4
ND N:HEA602 3.1 21.7 0.6
C2B N:HEA602 3.2 22.9 0.6
CD2 N:HIS376 3.2 25.6 1.0
N N:CYN606 3.3 24.9 0.4
N N:CYN606 3.4 26.4 0.6
CHC N:HEA602 3.4 21.8 0.6
C3B N:HEA602 3.4 21.2 0.6
CHC N:HEA602 3.4 21.6 0.4
CHB N:HEA602 3.5 22.4 0.4
C1C N:HEA602 3.5 19.4 0.6
CHD N:HEA602 3.6 22.6 0.4
CHA N:HEA602 3.6 22.7 0.4
C3A N:HEA602 3.6 21.1 0.6
C4D N:HEA602 3.9 24.3 0.6
C2A N:HEA602 4.0 22.6 0.6
CHA N:HEA602 4.0 25.2 0.6
ND1 N:HIS376 4.1 28.2 1.0
C4C N:HEA602 4.1 23.1 0.6
C2B N:HEA602 4.2 26.0 0.4
CG N:HIS376 4.2 25.0 1.0
C2C N:HEA602 4.2 19.0 0.4
C3A N:HEA602 4.2 22.9 0.4
C3B N:HEA602 4.2 23.8 0.4
C3C N:HEA602 4.2 23.6 0.4
C2D N:HEA602 4.2 21.5 0.4
C1D N:HEA602 4.2 23.1 0.6
C2A N:HEA602 4.3 21.1 0.4
C3D N:HEA602 4.3 22.7 0.4
CA N:GLY355 4.4 29.7 1.0
CMB N:HEA602 4.5 27.3 0.6
O N:HOH787 4.5 25.9 0.7
NE2 N:HIS290 4.7 18.7 0.4
CHD N:HEA602 4.7 22.4 0.6
CMA N:HEA602 4.8 25.0 0.6
C2C N:HEA602 4.8 19.4 0.6
C11 N:HEA602 4.9 23.5 0.6
CG1 N:VAL380 5.0 27.9 0.4

Reference:

A.Shimada, J.Baba, K.Shinzawa-Itoh, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidese in Cn-Bound Fully Reduced State at 50 K. To Be Published.
Page generated: Fri Aug 9 08:56:58 2024

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